1 /* Copyright (c) 2009 Peter Troshin
\r
3 * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0
\r
5 * This library is free software; you can redistribute it and/or modify it under the terms of the
\r
6 * Apache License version 2 as published by the Apache Software Foundation
\r
8 * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without
\r
9 * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache
\r
10 * License for more details.
\r
12 * A copy of the license is in apache_license.txt. It is also available here:
\r
13 * @see: http://www.apache.org/licenses/LICENSE-2.0.txt
\r
15 * Any republication or derived work distributed in source code form
\r
16 * must include this copyright and license notice.
\r
19 package compbio.engine;
\r
21 import static org.testng.Assert.assertEquals;
\r
22 import static org.testng.Assert.assertNotNull;
\r
23 import static org.testng.Assert.fail;
\r
25 import java.io.File;
\r
26 import java.io.IOException;
\r
27 import java.util.concurrent.TimeUnit;
\r
29 import org.testng.annotations.BeforeTest;
\r
30 import org.testng.annotations.Test;
\r
32 import compbio.engine.client.ConfiguredExecutable;
\r
33 import compbio.engine.client.Executable;
\r
34 import compbio.engine.local.AsyncLocalRunner;
\r
35 import compbio.metadata.AllTestSuit;
\r
36 import compbio.metadata.ChunkHolder;
\r
37 import compbio.metadata.JobSubmissionException;
\r
38 import compbio.metadata.ResultNotAvailableException;
\r
39 import compbio.runner.msa.ClustalW;
\r
40 import compbio.runner.msa.Muscle;
\r
42 public class FilePullerTester {
\r
44 public static String test_input = AllTestSuit.TEST_DATA_PATH_ABSOLUTE
\r
51 @BeforeTest(alwaysRun = true)
\r
52 public void init() {
\r
53 ClustalW clustal = new ClustalW();
\r
54 clustal.setInput(test_input);
\r
55 Muscle ms = new Muscle().setInput(test_input);
\r
56 Muscle ms2 = new Muscle().setInput(test_input);
\r
59 // For local execution use relavive
\r
60 ConfiguredExecutable<ClustalW> confClustal = Configurator
\r
61 .configureExecutable(clustal, Executable.ExecProvider.Local);
\r
62 ConfiguredExecutable<Muscle> confms = Configurator
\r
63 .configureExecutable(ms, Executable.ExecProvider.Local);
\r
65 ConfiguredExecutable<Muscle> confms2 = Configurator
\r
66 .configureExecutable(ms2, Executable.ExecProvider.Local);
\r
68 AsyncLocalRunner as = new AsyncLocalRunner();
\r
69 jobId = as.submitJob(confClustal);
\r
70 jobId2 = as.submitJob(confms);
\r
71 jobId3 = as.submitJob(confms2);
\r
73 ConfiguredExecutable<?> al = as.getResults(jobId);
\r
74 ConfiguredExecutable<?> al2 = as.getResults(jobId2);
\r
75 ConfiguredExecutable<?> al3 = as.getResults(jobId3);
\r
79 } catch (JobSubmissionException e) {
\r
80 e.printStackTrace();
\r
81 fail(e.getLocalizedMessage());
\r
82 } catch (ResultNotAvailableException e) {
\r
83 e.printStackTrace();
\r
84 fail(e.getLocalizedMessage());
\r
88 @Test(groups = { AllTestSuit.test_group_engine })
\r
89 public void testPull() {
\r
90 assertNotNull(jobId, "init() method failed!");
\r
91 String workDir = Configurator.getWorkDirectory(jobId);
\r
92 String statFile = workDir + File.separator + ClustalW.getStatFile();
\r
94 ChunkHolder ch = ProgressGetter.pull(statFile, 0);
\r
95 while (ch == null) {
\r
96 ch = ProgressGetter.pull(statFile, 0);
\r
101 chunk = ch.getChunk();
\r
102 assertNotNull(chunk);
\r
103 pos = ch.getNextPosition();
\r
104 ch = ProgressGetter.pull(statFile, pos);
\r
105 } while (chunk.length() > 0);
\r
107 // All consequent pulls just return empty chunk and same position =
\r
109 ch = ProgressGetter.pull(statFile, pos);
\r
111 assertEquals(ch.getChunk().length(), 0);
\r
112 // Output file size depends on the operation system fs!
\r
113 // assertEquals(ch.getNextPosition(), 668);
\r
115 ch = ProgressGetter.pull(statFile, pos);
\r
117 assertEquals(ch.getChunk().length(), 0);
\r
118 // Output file size depends on the operation system and fs!
\r
119 // assertEquals(ch.getNextPosition(), 668);
\r
123 @Test(groups = { AllTestSuit.test_group_engine })
\r
124 public void testGetDelay() {
\r
125 FilePuller fp = FilePuller.newFilePuller(Configurator
\r
126 .getWorkDirectory(jobId)
\r
127 + File.separator + "stat.log", 256);
\r
128 // default delay is 5 minutes
\r
129 assertEquals(fp.getDelayValue(TimeUnit.SECONDS), 5 * 60);
\r
130 long d = 1000 * 1000 * 1000L * 60; // 1m in nanoseconds
\r
131 fp.setDelay(d, TimeUnit.NANOSECONDS);
\r
132 assertEquals(fp.getDelayValue(TimeUnit.NANOSECONDS), d);
\r
133 assertEquals(fp.getDelayValue(TimeUnit.SECONDS), 60);
\r
134 assertEquals(fp.getDelayValue(TimeUnit.MINUTES), 1);
\r
137 @Test(groups = { AllTestSuit.test_group_engine }, dependsOnMethods = { "testPull" })
\r
138 public void testCache() {
\r
139 assertNotNull(jobId, "init() method failed!");
\r
140 assertNotNull(jobId2, "init() method failed!");
\r
141 assertEquals(PulledFileCache.getSize(), 1); // One is from previous test
\r
143 String statFile = Configurator.getWorkDirectory(jobId) + File.separator
\r
144 + ClustalW.getStatFile();
\r
145 String statFile2 = Configurator.getWorkDirectory(jobId2)
\r
146 + File.separator + Muscle.getStatFile();
\r
147 String statFile3 = Configurator.getWorkDirectory(jobId3)
\r
148 + File.separator + Muscle.getStatFile();
\r
150 ChunkHolder ch = ProgressGetter.pull(statFile, 0);
\r
151 assertEquals(PulledFileCache.getSize(), 1); // Still one as job has been
\r
152 // retrieved from cache
\r
153 ChunkHolder ch2 = ProgressGetter
\r
154 .pull(statFile2, 0, 5, TimeUnit.SECONDS); // 5
\r
156 assertEquals(PulledFileCache.getSize(), 2); // One is from previous test
\r
158 // Pull the first job completely
\r
159 while (ch == null) {
\r
160 ch = ProgressGetter.pull(statFile, 0);
\r
165 chunk = ch.getChunk();
\r
166 assertNotNull(chunk);
\r
167 pos = ch.getNextPosition();
\r
168 ch = ProgressGetter.pull(statFile, pos);
\r
169 } while (chunk.length() > 0);
\r
172 Thread.sleep(1000 * 6);
\r
173 } catch (InterruptedException e) {
\r
174 e.printStackTrace();
\r
175 fail(e.getMessage());
\r
177 // Elements are removed on put operation only
\r
178 assertEquals(PulledFileCache.getSize(), 2); // One is from previous test
\r
179 ChunkHolder ch3 = ProgressGetter.pull(statFile3, 0);
\r
180 // Now old element was removed, but new added, thus size remains
\r
182 assertEquals(PulledFileCache.getSize(), 2); // One is from previous test
\r
187 public void testGet() {
\r
189 FilePuller pp = FilePuller
\r
190 .newProgressPuller(AllTestSuit.TEST_DATA_PATH_ABSOLUTE
\r
191 + "percentProgress.txt");
\r
193 assertEquals(pp.getProgress(), 12);
\r
195 } catch (NumberFormatException e) {
\r
196 e.printStackTrace();
\r
197 fail(e.getMessage());
\r
198 } catch (IOException e) {
\r
199 e.printStackTrace();
\r
200 fail(e.getMessage());
\r